Fragile X syndrome (FXS) is the most common heritable cause of cognitive disability and autism. To date, there is no effective treatment for this disorder, nor a suitable animal model that recapitulates its pathogenesis. In this study, we have developed a high-throughput screening assay in induced pluripotent stem cell model of FXS, and used it to systematically screen a compound library for the ability to restore the molecular phenotype of the disease. Candidate treatments were assessed for their additive, long-term and genome-wide effects in neural cells, and evaluated using novel in vivo modeling platforms of differentiated FXS-affected transplants. Overall, our work offers new candidate drug therapies for FXS, and presents tools for the identification and analysis of disease modifying treatments.